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inter_CATI_omics
Hackathon_octobre2021
atelier_repro
Commits
069a1a5c
Commit
069a1a5c
authored
Oct 06, 2021
by
Frederique Bitton
Browse files
Delete config_para_TE.yaml
parent
de23ae7d
Pipeline
#42459
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in 1 minute and 23 seconds
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Snakemake/config_para_TE.yaml
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de23ae7d
tmp_dir
:
"
"
gff_file_ref
:
"
data/Col0_classic_refTEs_withoutOtherTargets_test.gff"
gff_file_sub
:
"
data/TAIR10_gene_test.gff3"
chr_list
:
"
data/Ath_chrs.txt"
# singularity images location
fastqc_bin
:
"
/work2/project/gafl/tools/containers/fastqc_V0.11.8.sif"
multiqc_bin
:
"
/work2/project/gafl/tools/containers/multiqc_v1.7.sif"
cutadapt_bin
:
"
/work2/project/gafl/tools/containers/cutadapt_v2.7.sif"
fastp_bin
:
"
/work2/project/gafl/tools/containers/fastp_0.20.0.sif"
samtools_bin
:
"
/work2/project/gafl/tools/containers/samtools_v1.9.sif"
bwa_bin
:
"
/work2/project/gafl/tools/containers/bwa_0.7.17.sif"
sambamba_bin
:
"
/work2/project/gafl/tools/containers/sambamba_v0.7.1.sif"
gatk4_bin
:
"
/work2/project/gafl/tools/containers/gatk4_v4.1.4.1.sif"
R_bin
:
"
/work2/project/gafl/tools/containers/R_base_V3.6.0.sif"
# bind Genotoul:
#BIND : "-B /work2/project/gafl,/work2/project/pangenometomate/"
# singularity modules only for genotoul
#MODULES : "module load system/singularity-3.5.3"
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